HEADER STRUCTURAL PROTEIN 12-DEC-22 8BYE TITLE FRAGMENT-LINKED STABILIZER FOR ERA - 14-3-3 INTERACTION (1075313) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 14-3-3 PROTEIN SIGMA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EPITHELIAL CELL MARKER PROTEIN 1,STRATIFIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ERALPHA PEPTIDE; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SFN, HME1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS 14-3-3, ERA, FRAGMENT LINKING, STABILIZATION, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.J.VISSER,E.M.F.VANDENBOORN,C.OTTMANN REVDAT 5 13-NOV-24 8BYE 1 REMARK REVDAT 4 13-SEP-23 8BYE 1 JRNL REVDAT 3 30-AUG-23 8BYE 1 REMARK REVDAT 2 09-AUG-23 8BYE 1 JRNL REVDAT 1 02-AUG-23 8BYE 0 JRNL AUTH E.J.VISSER,P.JAISHANKAR,E.SIJBESMA,M.A.M.PENNINGS, JRNL AUTH 2 E.M.F.VANDENBOORN,X.GUILLORY,R.J.NEITZ,J.MORROW,S.DUTTA, JRNL AUTH 3 A.R.RENSLO,L.BRUNSVELD,M.R.ARKIN,C.OTTMANN JRNL TITL FROM TETHERED TO FREESTANDING STABILIZERS OF 14-3-3 JRNL TITL 2 PROTEIN-PROTEIN INTERACTIONS THROUGH FRAGMENT LINKING. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 62 08004 2023 JRNL REFN ESSN 1521-3773 JRNL PMID 37455289 JRNL DOI 10.1002/ANIE.202308004 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2-4158 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 70541 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1695 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.3400 - 3.6600 0.97 5755 158 0.1729 0.1996 REMARK 3 2 3.6600 - 2.9100 0.97 5770 152 0.1597 0.1849 REMARK 3 3 2.9100 - 2.5400 0.98 5839 147 0.1623 0.2150 REMARK 3 4 2.5400 - 2.3100 0.97 5763 137 0.1542 0.1925 REMARK 3 5 2.3100 - 2.1400 0.95 5644 140 0.1573 0.1819 REMARK 3 6 2.1400 - 2.0200 0.97 5723 169 0.1543 0.2030 REMARK 3 7 2.0200 - 1.9100 0.97 5804 128 0.1842 0.2039 REMARK 3 8 1.9100 - 1.8300 0.97 5712 134 0.1937 0.2544 REMARK 3 9 1.8300 - 1.7600 0.97 5747 159 0.2050 0.2352 REMARK 3 10 1.7600 - 1.7000 0.97 5754 130 0.2182 0.2513 REMARK 3 11 1.7000 - 1.6500 0.96 5688 138 0.2292 0.2775 REMARK 3 12 1.6500 - 1.6000 0.95 5647 103 0.2596 0.2678 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 1950 REMARK 3 ANGLE : 1.136 2628 REMARK 3 CHIRALITY : 0.049 286 REMARK 3 PLANARITY : 0.010 340 REMARK 3 DIHEDRAL : 9.540 270 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8BYE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1292127371. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96546 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 153207 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 45.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.095 M HEPES (PH 7.3), PEG400 (28% REMARK 280 (V/V)), 0.19 M CACL2 AND 5% (V/V) GLYCEROL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.18550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.18550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 40.88600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.98350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.88600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.98350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 31.18550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.88600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 55.98350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 31.18550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.88600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 55.98350 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 -81.77200 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 31.18550 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 707 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 71 CD OE1 OE2 REMARK 470 GLU A 72 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 18 75.26 -105.93 REMARK 500 SER A 74 -122.27 -104.78 REMARK 500 GLU A 75 87.75 -169.58 REMARK 500 GLU A 76 74.23 -64.75 REMARK 500 HIS A 106 37.49 -146.24 REMARK 500 REMARK 500 REMARK: NULL DBREF 8BYE A 1 231 UNP P31947 1433S_HUMAN 1 231 DBREF 8BYE B 591 595 PDB 8BYE 8BYE 591 595 SEQADV 8BYE GLY A -4 UNP P31947 EXPRESSION TAG SEQADV 8BYE ALA A -3 UNP P31947 EXPRESSION TAG SEQADV 8BYE MET A -2 UNP P31947 EXPRESSION TAG SEQADV 8BYE GLY A -1 UNP P31947 EXPRESSION TAG SEQADV 8BYE SER A 0 UNP P31947 EXPRESSION TAG SEQRES 1 A 236 GLY ALA MET GLY SER MET GLU ARG ALA SER LEU ILE GLN SEQRES 2 A 236 LYS ALA LYS LEU ALA GLU GLN ALA GLU ARG TYR GLU ASP SEQRES 3 A 236 MET ALA ALA PHE MET LYS GLY ALA VAL GLU LYS GLY GLU SEQRES 4 A 236 GLU LEU SER CYS GLU GLU ARG ASN LEU LEU SER VAL ALA SEQRES 5 A 236 TYR LYS ASN VAL VAL GLY GLY GLN ARG ALA ALA TRP ARG SEQRES 6 A 236 VAL LEU SER SER ILE GLU GLN LYS SER ASN GLU GLU GLY SEQRES 7 A 236 SER GLU GLU LYS GLY PRO GLU VAL ARG GLU TYR ARG GLU SEQRES 8 A 236 LYS VAL GLU THR GLU LEU GLN GLY VAL CYS ASP THR VAL SEQRES 9 A 236 LEU GLY LEU LEU ASP SER HIS LEU ILE LYS GLU ALA GLY SEQRES 10 A 236 ASP ALA GLU SER ARG VAL PHE TYR LEU LYS MET LYS GLY SEQRES 11 A 236 ASP TYR TYR ARG TYR LEU ALA GLU VAL ALA THR GLY ASP SEQRES 12 A 236 ASP LYS LYS ARG ILE ILE ASP SER ALA ARG SER ALA TYR SEQRES 13 A 236 GLN GLU ALA MET ASP ILE SER LYS LYS GLU MET PRO PRO SEQRES 14 A 236 THR ASN PRO ILE ARG LEU GLY LEU ALA LEU ASN PHE SER SEQRES 15 A 236 VAL PHE HIS TYR GLU ILE ALA ASN SER PRO GLU GLU ALA SEQRES 16 A 236 ILE SER LEU ALA LYS THR THR PHE ASP GLU ALA MET ALA SEQRES 17 A 236 ASP LEU HIS THR LEU SER GLU ASP SER TYR LYS ASP SER SEQRES 18 A 236 THR LEU ILE MET GLN LEU LEU ARG ASP ASN LEU THR LEU SEQRES 19 A 236 TRP THR SEQRES 1 B 5 PHE PRO ALA TPO VAL HET TPO B 594 11 HET RY0 A 401 48 HETNAM TPO PHOSPHOTHREONINE HETNAM RY0 ~{N}-[3-(5-CARBAMIMIDOYLTHIOPHEN-3-YL)PHENYL]-1-(4- HETNAM 2 RY0 CHLORANYLPHENOXY)CYCLOBUTANE-1-CARBOXAMIDE HETSYN TPO PHOSPHONOTHREONINE FORMUL 2 TPO C4 H10 N O6 P FORMUL 3 RY0 C22 H20 CL N3 O2 S FORMUL 4 HOH *245(H2 O) HELIX 1 AA1 GLU A 2 ALA A 16 1 15 HELIX 2 AA2 ARG A 18 LYS A 32 1 15 HELIX 3 AA3 SER A 37 GLU A 71 1 35 HELIX 4 AA4 PRO A 79 SER A 105 1 27 HELIX 5 AA5 ASP A 113 ALA A 135 1 23 HELIX 6 AA6 ASP A 139 MET A 162 1 24 HELIX 7 AA7 ASN A 166 ILE A 183 1 18 HELIX 8 AA8 SER A 186 ALA A 203 1 18 HELIX 9 AA9 ASP A 204 LEU A 208 5 5 HELIX 10 AB1 SER A 209 THR A 231 1 23 LINK C ALA B 593 N TPO B 594 1555 1555 1.33 LINK C TPO B 594 N VAL B 595 1555 1555 1.32 CISPEP 1 SER A 105 HIS A 106 0 8.64 CRYST1 81.772 111.967 62.371 90.00 90.00 90.00 C 2 2 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012229 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008931 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016033 0.00000